Contacts of the strand formed by residues 367 - 373 (chain A) in PDB entry 4Y2H
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with LYS 367 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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327A GLU* 4.5 13.9 + - - -
358A ARG* 3.5 6.7 - - - +
359A TYR* 2.8 64.9 + - + +
364A GLN* 3.8 26.0 - - - +
365A GLU* 3.4 28.9 + - - +
366A GLU* 1.3 80.8 - - - +
368A THR* 1.3 65.3 + - - +
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Residues in contact with THR 368 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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357A LEU 3.5 10.1 + - - -
358A ARG* 3.8 30.5 + - - +
359A TYR* 5.0 2.5 - - - -
367A LYS* 1.3 80.0 + - - +
369A LYS* 1.3 67.5 + - - +
370A ASP* 5.7 4.0 - - - +
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Residues in contact with LYS 369 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231A MET 3.0 15.8 + - - -
232A GLY 4.7 0.7 - - - -
233A HIS* 3.0 30.4 + - - -
234A SER* 4.4 7.0 - - - +
324A TYR* 2.7 25.4 + - - +
325A LEU* 3.7 4.1 - - + -
326A ASN* 3.1 28.6 + - - +
357A LEU* 2.8 45.2 + - + +
359A TYR* 5.1 6.7 - - + -
368A THR* 1.3 79.8 + - - +
370A ASP* 1.3 66.5 + - - +
371A PHE* 3.6 32.9 - - + -
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Residues in contact with ASP 370 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234A SER* 3.4 24.3 + - - -
354A ARG* 4.7 9.7 + - - +
355A VAL 3.4 3.1 - - - -
356A LEU* 3.3 36.4 - - + +
357A LEU 4.1 1.4 + - - +
368A THR* 5.7 3.6 - - - +
369A LYS* 1.3 84.5 + - - +
371A PHE* 1.3 63.6 + - - +
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Residues in contact with PHE 371 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233A HIS* 5.0 1.3 - + - -
234A SER* 3.2 14.8 - - - +
235A GLU 3.9 17.5 - - - -
236A ILE* 3.4 19.7 - - + -
323A LEU* 3.8 30.3 - - + -
324A TYR* 3.5 37.2 - - + -
325A LEU* 5.6 0.7 - - + -
354A ARG* 3.4 10.4 - - - +
355A VAL* 2.8 42.6 + - + +
357A LEU* 3.9 22.4 - - + -
369A LYS* 3.6 40.2 - - + -
370A ASP* 1.3 75.6 - - - +
372A ALA* 1.3 60.6 + - - +
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Residues in contact with ALA 372 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234A SER 3.0 7.9 + - - +
235A GLU* 3.4 7.7 - - + +
236A ILE* 3.0 18.0 + - - -
346A SER* 4.7 4.9 - - - +
352A ARG* 3.6 34.5 + - - +
353A LEU 3.4 8.3 - - - +
354A ARG* 5.0 4.7 - - + -
371A PHE* 1.3 75.3 - - - +
373A MET* 1.3 66.4 + - - +
374A GLU 3.2 0.3 + - - -
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Residues in contact with MET 373 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159A TYR* 3.5 30.1 - - + +
160A GLY 4.7 1.3 - - - +
163A HIS* 3.4 49.6 - - + +
236A ILE* 3.5 36.4 - - + +
238A VAL* 4.0 18.4 - - + -
321A ALA* 5.0 0.9 - - + -
352A ARG* 3.0 31.0 + - + +
353A LEU* 2.8 31.7 + - + +
372A ALA* 1.3 70.0 - - - +
374A GLU* 1.3 80.8 + - - +
375A ASP* 4.4 0.2 - - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il